Small RNA tools

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General organization[edit]

The small RNA webpage can be accessed either from the home webpage of the Listeriomics website or by double-clicking on a small RNA in the genome viewer.

Printscreen of the Gene webpage of the Listeriomics website


Small RNA search and selection

In this list, all the small RNA available in Listeria monocytogenes EGD-e strain are displayed. One can search for a small RNA. A click on an element of the list will display all related information on the Small RNA information panel.

Omics selection panel

For each Listeria small RNA two different information panels are available.

  • General information: The position of the small RNA, possible regulation, DNA sequence and predicted secondary structure.
  • Expression atlas: It shows in which transcriptomics datasets the selected small RNA is differently expressed. The cut-off on the Log(Fold Change) value for detecting such elements can be changed by the user.
Small RNA information panel

The panel in which all information will be displayed

How-to access Small RNA information ?[edit]

Small RNA general information panel of the Small RNA webpage
Click on General information on the Omics selection panel
  • Genome viewer: Displays the small RNA in the genome viewer to see surrounding genome features.
  • General information: Every general information available on small RNA position, and study in which it was discovered.
  • Supplementary information: All supplementary information available from all the studies in which the small RNA was detected.
  • DNA Sequences: DNA sequences can be accessed here and saved to fasta file or sent directly to Blast.
  • Predicted secondary structure: Predicted secondary structure at 37°C of the small RNA using UNAFold software.
Sequence information panel of the Small RNA webpage
DNA sequences can be accessed here and saved to fasta file or sent directly to Blast.

Is my Small RNA transcribed ?[edit]

Expression atlas panel of the Small RNA webpage
Click on Expression Atlas on the Omics selection panel
  • Cut-off selection: Select the value of Log(Fold Change) used to detect differential expression.
  • Send to Genome viewer of Heatmap viewer: Display selected datasets in the genome viewer in which the small RNA will be highlighted, or to the heatmap viewer to show the values of Log(Fold-change).
  • Datasets in which the gene is over-expressed: List of relative value expression data in which the small RNAis over-expressed (i.e. Log(FC) > cut-off).
  • Datasets in which the gene is under-expressed: List of relative value expression data in which the small RNAis under-expressed (i.e. Log(FC) < - cut-off).
  • Datasets in which the gene has no differential expression: List of relative value expression data in which the small RNAis not differentially expressed (i.e. - cut-off < Log(FC) < cut-off).

Summary of Small RNA studies in Listeria monocytogenes EGD-e[edit]

In the past decade, noncoding RNAs in Listeria have been studied in detail [1] [2] [3] [4] [5] [6].

One study concerns strain 10403S [4], and all the other studies concern the EGD-e strain.

Altogether, 305 noncoding RNA elements are reported in Listeria monocytogenes EGD-e. They are separated in three groups:

  • 155 sRNAs (acting mainly in trans)
  • 46 cis regulatory elements (cisRegs)
  • 104 antisense RNAs (asRNAs)

Tables summarizing all the small RNAs observed can be accessed in the small RNAs summary webpage. This page can be accessed from the home webpage of the Listeriomics website.

Printscreen of the Small RNAs summary webpage of the Listeriomics website


Small RNA type selection:

Type of small RNA to display:

  • sRNAs
  • cisRegs
  • asRNAs
Small RNAs summary table

Table with different information on each small RNA:

  • Position
  • If a transcription start site has been found in [6]
  • In which study it has been first discovered
  • In which other study it has been observed

By clicking on a small RNA, the small RNA webpage will open to give more information.

References[edit]

Template:References
  1. Christiansen JK, Nielsen JS, Ebersbach T, Valentin-hansen P, Søgaard- Andersen L, Kallipolitis BH. 2006. Identification of small Hfq-binding RNAs in Listeria monocytogenes. RNA 12:1383–1396.
  2. Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P. 2007. Identification of new noncoding RNAs in Listeria monocytogenes and pre- diction of mRNA targets. Nucleic Acids Res. 35:962–974.
  3. Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Bar- thelemy M, Vergassola M, Nahori MA, Soubigou G, Régnault B, Cop- pée JY, Lecuit M, Johansson J, Cossart P. 2009. The Listeria transcrip- tional landscape from saprophytism to virulence. Nature 459:950–956.
  4. 4.0 4.1 Oliver HF, Orsi RH, Ponnala L, Keich U, Wang W, Sun Q, Cartinhour SW, Filiatrault MJ, Wiedmann M, Boor KJ. 2009. Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. BMC Genomics 10:641.
  5. Mraheil MA, Billion A, Mohamed W, Mukherjee K, Kuenne C, Pischi- marov J, Krawitz C, Retey J, Hartsch T, Chakraborty T, Hain T. 2011. The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages. Nucleic Acids Res. 39:1–14.
  6. 6.0 6.1 Wurtzel O, Sesto N, Mellin JR, Karunker I, Edelheit S, Bécavin C, Archambaud C, Cossart P, Sorek R. 2012. Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol. Syst. Biol. 8:1–14. [http://dx.doi.org/10.1038/msb.2012.11.